{"id":"https://openalex.org/W2170694711","doi":"https://doi.org/10.1142/s021972000900445x","title":"A PROBABILISTIC FRAMEWORK TO IMPROVE MICRORNA TARGET PREDICTION BY INCORPORATING PROTEOMICS DATA","display_name":"A PROBABILISTIC FRAMEWORK TO IMPROVE MICRORNA TARGET PREDICTION BY INCORPORATING PROTEOMICS DATA","publication_year":2009,"publication_date":"2009-12-01","ids":{"openalex":"https://openalex.org/W2170694711","doi":"https://doi.org/10.1142/s021972000900445x","mag":"2170694711","pmid":"https://pubmed.ncbi.nlm.nih.gov/20014473"},"language":"en","primary_location":{"id":"doi:10.1142/s021972000900445x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000900445x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100338392","display_name":"Jingjing Li","orcid":"https://orcid.org/0000-0002-8875-4725"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"JINGJING LI","raw_affiliation_strings":["Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000236616","display_name":"Renqiang Min","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"RENQIANG MIN","raw_affiliation_strings":["Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113493758","display_name":"Anthony J. Bonner","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"ANTHONY BONNER","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009847434","display_name":"Zhaolei Zhang","orcid":"https://orcid.org/0000-0002-7303-6472"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"ZHAOLEI ZHANG","raw_affiliation_strings":["Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100338392"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":null,"apc_paid":null,"fwci":1.1634,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.81312636,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"07","issue":"06","first_page":"955","last_page":"972"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/complementarity","display_name":"Complementarity (molecular biology)","score":0.7466787099838257},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.6908388137817383},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5971454381942749},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.585474967956543},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5710365176200867},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4845260977745056},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.41223689913749695},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31834834814071655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2621994912624359},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18212231993675232},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14144542813301086}],"concepts":[{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.7466787099838257},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.6908388137817383},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5971454381942749},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.585474967956543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5710365176200867},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4845260977745056},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.41223689913749695},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31834834814071655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2621994912624359},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18212231993675232},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14144542813301086}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018390","descriptor_name":"Gene Targeting","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018390","descriptor_name":"Gene Targeting","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018390","descriptor_name":"Gene Targeting","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1142/s021972000900445x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000900445x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:20014473","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20014473","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.731.7483","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.731.7483","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.toronto.edu/%7Ebonner/papers/jbcb09.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1953939973","https://openalex.org/W1963952972","https://openalex.org/W1966241066","https://openalex.org/W1978270504","https://openalex.org/W1978337436","https://openalex.org/W1990868443","https://openalex.org/W2014946489","https://openalex.org/W2017199818","https://openalex.org/W2017270642","https://openalex.org/W2042004955","https://openalex.org/W2045234988","https://openalex.org/W2045656233","https://openalex.org/W2050869737","https://openalex.org/W2083381199","https://openalex.org/W2084407186","https://openalex.org/W2085316301","https://openalex.org/W2089142809","https://openalex.org/W2096373458","https://openalex.org/W2117391818","https://openalex.org/W2120456037","https://openalex.org/W2130362663","https://openalex.org/W2149386535","https://openalex.org/W2163199119","https://openalex.org/W2164683872","https://openalex.org/W2169600668","https://openalex.org/W4247690662"],"related_works":["https://openalex.org/W2521519254","https://openalex.org/W3139833644","https://openalex.org/W3123110765","https://openalex.org/W4383553409","https://openalex.org/W2212953222","https://openalex.org/W2104948296","https://openalex.org/W1735800226","https://openalex.org/W4285172739","https://openalex.org/W3123208392","https://openalex.org/W4372316851"],"abstract_inverted_index":{"Due":[0],"to":[1,69,129,132,140],"the":[2,47,53,59,98,106,110,133,137,142,145,167,176],"difficulties":[3],"in":[4,10,170],"identifying":[5],"microRNA":[6],"(miRNA)":[7],"targets":[8,139],"experimentally":[9],"a":[11,66,91,117,125],"high-throughput":[12],"manner,":[13],"several":[14],"computational":[15],"approaches":[16],"have":[17],"been":[18,35],"proposed.":[19],"To":[20],"this":[21],"date,":[22],"most":[23],"leading":[24],"algorithms":[25],"are":[26],"based":[27],"on":[28,159],"sequence":[29,74,88],"information":[30],"alone.":[31],"However,":[32],"there":[33],"has":[34,156],"limited":[36],"overlap":[37],"between":[38,90,181],"these":[39],"predictions,":[40,121],"implying":[41],"high":[42,104],"false-positive":[43],"rates,":[44],"which":[45],"underlines":[46],"limitation":[48],"of":[49,56,109,119,136,144,163],"sequence-based":[50],"approaches.":[51],"Considering":[52],"repressive":[54],"nature":[55],"miRNAs":[57],"at":[58],"mRNA":[60,96,111,134,160,164,182],"translational":[61,153],"level,":[62,78],"here":[63],"we":[64,122],"describe":[65],"probabilistic":[67,127],"model":[68,128],"make":[70],"predictions":[71],"by":[72],"combining":[73],"complementarity,":[75],"miRNA":[76,92,99,171],"expression":[77,100,135,183],"and":[79,93,105,184],"protein":[80,107,185],"abundance.":[81,186],"Our":[82,149],"underlying":[83],"assumption":[84],"is":[85,166],"that,":[86],"given":[87],"complementarity":[89],"its":[94],"putative":[95],"targets,":[97],"level":[101],"should":[102,112],"be":[103,113],"abundance":[108],"low.":[114],"Having":[115],"identified":[116],"set":[118],"confident":[120,138],"then":[123],"built":[124],"second":[126],"trace":[130],"back":[131],"investigate":[141],"mechanisms":[143],"miRNA-mediated":[146],"post-transcriptional":[147],"regulation.":[148,172],"results":[150],"suggest":[151],"that":[152],"repression":[154],"(which":[155],"no":[157],"effect":[158],"level),":[161],"instead":[162],"degradation,":[165],"dominant":[168],"mechanism":[169],"This":[173],"observation":[174],"explained":[175],"previously":[177],"observed":[178],"discordant":[179],"correlation":[180]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
